Tutorial

The search algorithm scans each transcript and for each subsequence of length 7, the length of each motif, calculate its matrix similarity score (MSS). The MSS is defined as MSS = current_score – mimimum_score / maximum_score – minimum score. This will provide a value between 0 and 1 where 1 is the canonical motif. The score_current is defined as the product of each probability to observe a given nucleotide at a given position in the PWM. The score_maximum is the product of each maximum probability value in the PWM at each position. The score_minimum is the product of each minimum probability value in the PWM at each position.

Independently, the sum of all MSS score for each 4^7 possible substrings (k-mer) was calculated. A score, MSS’, is calculated by sequentially adding the MSS value of each k-mer incrementally. A score MSS’ % is obtained by dividing, for each k-mer, its MSS’ by the sum of all MSS’. A threshold can thus be calculated by taking the MSS scores representing up to 50% of all possible scores, by steps of 5%.

As shown in the figure, when searching for a given RBP motif (A) in a specific transcript (B), we can rapidly scan for each k-mer (C) and directly look it up in a table (D) in constant time, through the use of a dictionary, and populate the database with substrings passing the threshold as putative motif instances (E).

This tool allows you to search the database for a specific RBP, at a specific similarity threshold between the PWM and the subsequence, for which you would like to know all its putative instances in all the coding and non-coding transcripts of the selected organism.

Simply select your organism and your RBP of interest. The slider allows you to select the MMS' percent that will be used as the threshold. The database contains all motif instances with matrix similarity scores adding to a MSS' of 50% in increments of 5%. As some motifs of a given RBP might not add enough weight to the MSS', some thresholds can return identical results. The number of results (instances) that will be returned at each step is indicated.

This tool allows you to search the database for a specific combination of attributes in a given species for which you would like to know all putative RBP motif instances.

Simply select your organism and your biotype or region of interest. The motif status option allows the user to filter the database for only RBP that have direct or indirect motif evidence as assessed by Ray et al. Nature 2013 or to include every RBP motif available in the database. When an attribute is incompatible with other selections, it is shown as a blocked (unclickable and greyed out) NA. When selecting the protein coding biotype, the region NA corresponds to the Ensembl annotation for unavailable information, as such it is selectable. D. melanogaster annotation does not have transcript biotypes that differ from their corresponding gene biotype, therefore the option is removed when this species is selected. The number of results (instances) that will be returned for each combination is indicated.

When clicking on a gene ID, you are brought to the gene level detail page. This page will show the putative binding site of the RBP on the line it was clicked for that gene (i.e. if you click on ENSG000000000003 with RBP A1CF, you will see all motifs instances of A1CF in all isoforms of the TSPAN6 gene).

When clicking on a transcript ID, you are brought to the transcript level detail page. This page will show the putative binding site of the RBP on the line it was clicked for that isoform only (i.e. if you click on ENST00000373020 with RBP A1CF you will see all motifs instances of A1CF in this specific isoform of the TSPAN6 gene).

For a selected transcript, the 2-D structure, calculated by RNAfold with default argument, will also be shown. Please note that the structure is only shown for transcripts shorter than 30,000 nucleotides. For transcripts longer than a few thousand nucleotides, depending on your browser and system, the rendering may be slow. You may always click on the DOT-BRACKET button to download the sequence of structure of the transcript.